In 1944 Colgate enlisted in the merchant marine. After Hiroshima, the captain called upon him to "tell us what it means." At that time what he explained was strictly confidential, most of all the description of nuclear fission.

After being discharged in 1946, Colgate returned to Cornell University. He then completed a Bachelor of Science and a PhD in nuclear physics, taking up a position as postdoctoral fellow at Berkeley.